Method for determining quinolon resistance of tubercle bacilli

ABSTRACT

A novel mutation in the gyrase A gene involved in quinolon resistance phenotype acquisition of tubercle bacillus is identified and utilized to provide a method and kit for determining quinolon resistance of tubercle bacillus.

BACKGROUND OF THE INVENTION

[0001] 1. Field of the Invention

[0002] The present invention relates to a method and kit for determining quinolon resistance of srtains of tubercle bacilli (Mycobacterium tuberculosis), more specifically, a method and kit for determining quinolon resistance by detecting a novel mutation in the gyrase A gene, which imparts the quinolon resistance phenotype to tubercle bacilli.

[0003] 2. Description of the Related Art

[0004] Drug resistance phenotype acquisition mechanisms of bacteria include (1) such change of the cell wall structure that permeation of a drug into a cell should be blocked, (2) acquisition of a gene coding for an enzyme that decomposes or inactivates a drug, (3) change of a compound in a cell as a target of drug and so forth. Acquisition of these phenotypes are acheived by transmission among bacteria via transposable genetic elements such as plasmid and transposon, change of chromosomes or the like.

[0005] Acquisition of resistance phenotype to drugs (hereinafter, referred to as “antituberculous drug”) by Mycobacterium tuberculosis (hereinafter, also referred to as “tubercle bacilli”) is attributable to a spontaneous chromosomal mutation (A. Telenti, Tuberculosis, 1997, 18 (1): 55-64). For example, the mechanism of resistance of tubercle bacilli to rifampicin, which is an antituberculous drug, is resulted from nucleotide substitution occurring in the gene encoding the RNA polymerase β subunit protein, which is a target substance of rifampicin (A Telenti et al., Lancet, 1993, 341: 647-650). Furthermore, nucleotide substitution in the rpsl and rrs genes or the like induces streptomycin resistance (Y. Suzuki, et al., J. Applied. Microbiol., 1997, 83: 634-640). Thus, mechanisms for acquisition of resistance phenotype by a mutation in a gene involved in each target molecule exist for some antituberculous drugs.

[0006] Accordingly, most of drug resistance phenotype acquisition mechanisms of tubercle bacilli are explained based on spontaneous mutations.

[0007] In Escherichia coli, bacteria belonging to the genus Staphylococcus and so forth, quinolon resistance is acquired by introduction of a nucleotide mutation into a gene encoding the DNA gyrase activity, topoisomerase IV activity or a membrane integral protein involved in uptake and excretion of a substance into and from a cell (Cambau E., et al., Res. Microbiol., 1996, 147: 52-59; Ferrero L., et al., Antimicrob. Agents Chemother., 1995, 39: 1554-1558) or the like. One of the target compounds of quinolon is gyrase A, and a mutation in the gyrase A gene greatly contributes to resistance to clinically important quinolon molecular species (ciprofloxacin, ofloxacin etc., Cambau E., et al., J. Infect. Dis., 1994, 170: 479-483).

[0008] There have also been reported several mutations in the gyrase A gene involved in acquisition of quinolon resistance phenotype in tubercle bacilli (Antimicrob. Agents Chemother., 1996, 40 (8), 1768-1774; J. Infect. Dis., 1996, 174, 1127-1130; Eur. J. Clin. Microbiol. Infect. Dis., 1997, 16, 395-398; J. Infect. Dis., 2000, 182, 517-525).

SUMMARY OF THE INVENTION

[0009] An object of the present invention is to provide a method and kit for determining quinolon resistance of tubercle bacilli by identifying a novel mutation in the gyrase A gene involved in acquisition of quinolon resistance phenotype in tubercle bacilli and utilizing the mutation.

[0010] The inventors of the present invention assiduously studied in order to achieve the aforementioned object. As a result, they found a novel mutation imparting a quinolon resistance phenotype in the gyrase A gene sequence of tubercle bacilli and accomplished the present invention.

[0011] That is, the present invention provides the followings.

[0012] (1) A method for determining quinolon resistance of a Mycobacterium tuberculosis strain by detecting a mutation in a gyrase A gene of the bacterial strain, wherein the mutation is substitution of another amino acid residue for an amino acid residue corresponding to the 89th aspartic acid residue in an amino acid sequence encoded by the gyrase A gene.

[0013] (2) The method according to (1), wherein the other amino acid residue is an asparagine residue.

[0014] (3) The method according to (1) or (2), wherein the amino acid sequence encoded by the gyrase A gene is the amino acid sequence of SEQ ID NO: 4 or an amino acid sequence of SEQ ID NO: 4 including substitution, deletion or insertion of one or several amino acid residues.

[0015] (4) The method according to any one of (1) to (3), wherein the mutation is substitution of T for G that is the first nucleotide of a codon coding for an aspartic acid residue.

[0016] (5) The method according to (4), wherein the mutation occurs at a position corresponding to the 530th nucleotide in the nucleotide sequence of SEQ ID NO: 3.

[0017] (6) The method according to any one of (1) to (5), further comprising detecting a substitution of A for a base corresponding to G at the 545th position in the nucleotide sequence of SEQ ID NO: 3.

[0018] (7) A kit for determining quinolon resistance of a Mycobacterium tuberculosis strain by detecting a mutation in a gyrase A gene of the bacterial strain, comprising an oligonucleotide for detecting a substitution of another amino acid residue for an amino acid residue corresponding to the 89th aspartic acid residue in an amino acid sequence encoded by the gyrase A gene.

[0019] A novel mutation in the gyrase A gene involved in quinolon resistance phenotype acquisition by tubercle bacilli was identified by the present invention. By utilizing this mutation, a novel method and kit for determining quinolon resistance of tubercle bacilli are provided.

BRIEF EXPLANATION OF THE DRAWINGS

[0020]FIG. 1 shows alignment of nucleotide sequences of gyrA genes from strains of tubercle bacilli resistant to quinolon.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0021] Hereafter, the present invention will be explained in detail.

[0022] The present invention provides a method for determining quinolon resistance of a tubercle bacillus strain by detecting a mutation in the gyrase A gene (hereinafter, referred to as “gyrA”) of the bacterial strain. Within the reported nucleotide sequence of the gyrA gene of wild tubercle bacillus strain (GenBank locus MSGGYRAB, accession L27512.1 GI: 1107467), the sequence of nucleotide numbers 2041-4923 is shown as SEQ ID NO: 3. Further, an amino acid sequence encoded by the nucleotide sequence is shown as SEQ ID NO: 4. The amino acid sequence is shown in both of SEQ ID NOS: 3 and 4.

[0023] The method of the present invention is characterized in that the mutation in the aforementioned gyrA gene is a substitution of another amino acid residue for an amino acid residue corresponding to the 89th aspartic acid residue in the amino acid sequence encoded by the gyrA gene. FIG. 1 shows comparison of nucleotide sequences of a region around the mutation point. Further, a nucleotide sequence of the aforementioned region in the gyrA gene of a wild strain is shown as SEQ ID NO: 1. The amino acid sequence encoded by this sequence is shown as SEQ ID NO: 2. SEQ ID NO: 1 corresponds to the nucleotide numbers 511-560 in the nucleotide sequence including the gyrA gene shown as SEQ ID NO: 3. Further, the amino acid sequence of SEQ ID NO: 2 corresponds to the amino acid numbers 83-98 in the amino acid sequence encoded by the gyrA gene and shown as SEQ ID NO: 4.

[0024] As the aforementioned other amino acid residue, an asparagine residue can be mentioned. As a mutation in the gyrA gene that induces a mutation for substituting an asparagine residue for the aspartic acid residue, substitution of T for G that is the first nucleotide of a codon coding for an aspartic acid residue can be mentioned. A specific example of this mutation is a mutation occurring at a position corresponding to the 530th nucleotide in the nucleotide sequence of the gyrA gene shown as SEQ ID NO: 3.

[0025] The nucleotide or amino acid numbers in the nucleotide sequence or the amino acid sequence shown as SEQ ID NO: 3 or 4 may be changed due to a mutation in the gyrA gene occurring at a position that is not within a codon corresponding to the 89th aspartic acid residue. A gyrase A having such a mutation has an amino acid sequence including substitution, deletion or insertion of one or several amino acids in the amino acid sequence shown as SEQ ID NO: 4. The present invention can also be applied to a gene coding for the gyrase A including such a mutation so long as the mutation is involved in quinolon resistance. The expressions “amino acid residue corresponding to the 89th aspartic acid residue” and “position corresponding to the 530th nucleotide” refer to an amino acid residue or a nucleotide residue corresponding to such a position in the sequence shown as SEQ ID NO: 3 or 4 when the nucleotide numbers or amino acid numbers are changed as described above. For example, when the first amino acid residue of SEQ ID NO: 4 is deleted, an amino acid residue corresponding to the 89th aspartic acid residue means an aspartic acid residue that is the 88th amino acid residue from the N-terminus.

[0026] In the present invention, known mutations in the gyrA gene involved in quinolon resistance and/or mutations yet to be found in future may be detected in addition to the substitution of an amino acid residue corresponding to the 89th aspartic acid residue. As such mutations, there can be mentioned substitution of A for a base corresponding to G at the 545th position in SEQ ID NO: 3.

[0027] Mutations in the gyrA gene of tubercle bacillus can be detected in the same manner as in usual mutation detecting methods so long as a single nucleotide polymorphism can be detected. For example, there can be mentioned a method for detecting a mutation by directly determining the nucleotide sequence of the gyrA gene. Further, examples of a method for detecting a mutation utilizing PCR include methods such as the template-directed dye-terminator incorporation method (Chen, X. et al., Proc. Natl. Acad. Sci. USA, 20, 10756-10761 (1997)), the dye-labeled oligonucleotide ligation method (Chen, X. et al., Genome Res., 5, 549-556 (1998)), the molecular beacon method (Tyagi, S. et al., Nat. Biotechnol., 1, 49-53 (1998)), the dynamic allele-specific hybridization method (Howellm, W. M. et al., Nat. Biotechnol., 1, 87-88 (1998)) and so forth.

[0028] Further, as methods that do not utilize PCR, there can be mentioned the padlock probe method developed by Mats Nilsson et al. in 1994 (Nilsson, M. et al., Science, 5181, 2085-2088 (1994)) and modified by Paul M. Lizardi et al. (Lizardi, P. et al., Nat. Genet., 3, 225-232 (1998)), the invader assay method (WO94/29482) developed by Victor Lyamichev and so forth.

[0029] Furthermore, as other methods for detecting a single nucleotide polymorphism, the Luminex method utilizing flow cytometry and methods utilizing matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOFMS) are also known and can be used for the present invention.

[0030] Further, microarray methods (WO95/11995, U.S. Pat. No. 5,837,832), which are widely used in recent years, such as the single base sequencing on oligomicroarray method (Drmanac, R. et al., Genomics, 2, 114-128 (1989)) can also be used. The microarray methods are techniques in which a large number of capture nucleic acids are immobilized on a solid phase, a labeled target nucleic acid is hybridized with the capture nucleic acids to be captured, and the presence or absence or existence ratio of the target nucleic acid is analyzed exhaustively.

[0031] As an example of methods preferably used in the present invention, a method of detecting a target mutation in the gyrA gene by using an oligonucleotide immobilized on a substrate will be shown below.

[0032] As the oligonucleotide immobilized on the substrate, used is an oligonucleotide having a nucleotide sequence of a region including the position of the aforementioned mutation in the gyrA gene (hereinafter, referred to as “capture oligo”).

[0033] When the capture oligo is designed, it is usually preferred that a position corresponding to the aforementioned mutation included in the capture oligo should exist in the center portion of the capture oligo. When the capture oligo is too short, detection of the hybridization becomes difficult. When it is too long, inhibition of the hybridization due to a sequence unique to that type does not occur. Therefore, a length in the range of 10 to 24 nucleotides is preferred. Further, when there is a secondary structural failure that negatively affects the hybridization in a process of hybrid formation of the capture oligo and a target described later, a spacer or a nucleotide that does not form a hydrogen bond with any nucleotide can be introduced into the oligonucleotide sequence to avoid the aforementioned failure.

[0034] Although DNA is usually used as the capture oligo, a peptide nucleic acid (PNA) may also be used. Since a hybrid formed by a peptide nucleic acid with a nucleic acid derived from a test human genome has a higher Tm (melting temperature) in comparison with that obtained by using an oligonucleotide, it is expected that a stable hybridization signal can be obtained. The peptide nucleic acid can be readily synthesized by using a usual peptide synthesizer.

[0035] Synthesis of the oligonucleotide, preparation of chromosomal DNA, hybridization and PCR can be performed according to usual methods well known to those skilled in the art (refer to Maniatis, T. et al., “Molecular Cloning A Laboratory Manual, Second Edition”, Cold Spring Harbor Laboratory Press (1989)). Further, the oligonucleotide can be synthesized by using a commercially available DNA synthesizer.

[0036] Material of the substrate on which the oligonucleotide is immobilized is not particularly limited so long as the oligonucleotide can be stably immobilized thereon. However, for example, glass, synthetic resins such as polycarbonate and plastic can be mentioned. Although shape of the substrate is not also particularly limited, a plate-like or film-like substrate can be mentioned. The substrate preferably has a uniform and planar surface.

[0037] The oligonucleotide can be immobilized on the substrate by using a method used in a usual hybridization method such as physical adsorption, electrical coupling and formation of a molecular covalent bond. For example, there can be mentioned a method using a substrate of which surface is coated with a compound having a carbodiimide group or an isocyanate group (Japanese Patent Laid-open Publication (Kokai) No. 08-023975). The substrate coated with a compound having a carbodiimide group or an isocyanate group on the surface thereof can be prepared by coating the substrate surface with a macromolecular compound having a carbodiimide group or an isocyanate group. The oligonucleotides can be immobilized with a covalent bond on the substrate by irradiating with a ultraviolet ray. Further, as a linker for bonding the carbodiimide group or isocyanate group and the oligonucleotide, a compound having an amino group or an imino group having high reactivity with the carbodiimide group or isocyanate group is used. In the case of imino group, the compound can be bonded with a carbodiimide group or an isocyanate group by polymerizing thymine to either one of the ends of capture oligo.

[0038] The oligonucleotide can be immobilized on the substrate by, for example, spotting an oligonucleotide solution on the substrate by using a spotting machine. Usually, the oligonucleotide solution is preferably spotted in a substantially circular shape.

[0039] Further, multiple kinds of oligonucleotide are each usually spotted at multiple positions on a single substrate, and these spots are preferably arranged in a grid pattern. When the spot size is 1000 μm in diameter, the total number of spots is preferably 1600 spots/cm² or less and 40×40 or less of spots are preferably provided when they are spotted in a square pattern. Further, when the spot size is 10 μm in diameter, the total number is preferably 400 spots/cm² or less, and 20×20 or less of spots are preferably provided when they are spotted in a square pattern. Further, when the vertical and horizontal sizes of the pattern are different, the numbers of the spots along the vertical and horizontal directions may be adjusted depending on shape of the pattern.

[0040] The presence or absence of a specific mutation in the gyrA gene can be determined by hybridizing a nucleic acid fragment probe including a region corresponding to the position of the aforementioned mutation in the gyrA gene of chromosomal DNA of tubercle bacillus (referred to as “nucleic acid probe”) with a wild type capture oligo and a mutant capture oligo and examining with which type of capture oligo the probe hybridized. That is, to which drug the strain has resistance can be detected depending on the hybridization position on the substrate.

[0041] The nucleic acid can be prepared from tubercle bacilli in the same manner as in a usual method for preparing nucleic acids from bacteria. For example, DNA can be prepared according to the method described in Maniatis, T. et al., “Molecular Cloning A Laboratory Manual, Second Editions”, Cold Spring Harbor Laboratory Press (1989).

[0042] The nucleic acid probe can be prepared by amplifying a nucleic acid by using primers designed based on the nucleotide sequence of the capture oligo. Although DNA is usually used as the nucleic acid probe, RNA may also be used. As the method for amplifying a nucleic acid, there can be mentioned, for example, a method of amplifying a nucleic acid as DNA by polymerase chain reaction (PCR) and a method of amplifying a nucleic acid as RNA by the in vitro transcription method.

[0043] The primers used in PCR are designed so that the nucleic acid probe should include a specific mutation site in the gyrA gene and sequences on both sides thereof. As such primers, there can be mentioned oligonucleotides having the nucleotide sequences shown as SEQ ID NOS: 5 and 6.

[0044] If a primer is labeled beforehand, a labeled nucleic acid probe can be obtained. The nucleic acid probe may also be labeled during or after the nucleic acid amplification reaction. As a labeling substance, labeling substances similar to those used for a probe employed in usual hybridization such as a fluorescence substance or hapten can be used. Specific examples of the fluorescence substance include fluorescein (FITC), Rhodamine, phycoerythrin (PE), Texas Red, cyanine fluorescent dyes and so forth. Specific examples of the hapten include biotin, digoxigenin (Dig), dinitrophenyl (DNP) and so forth.

[0045] The primers for preparing a nucleic acid probe can be included in a kit for determining quinolon resistance of tubercle bacilli together with a substrate on which the oligonucleotide is immobilized.

[0046] The hybridization can be performed in the same manner as in usual nucleic acid hybridization. A specific method will be exemplified below.

[0047] A nucleic acid probe is added to a mixed solution containing a salt solution such as SSC (standard saline citrate), a blocking solution containing sodium dodecylsulfate (SDS), bovine serum albumin (BSA) or the like and additives for promoting a hybridization reaction. When the target is a double strand, denaturation is performed by heating or the like. A nucleic acid probe solution is added onto a substrate in an amount of several μL and heated for several hours (usually 37-70° C.) to form a hybrid between an oligonucleotide immobilized on the substrate and the nucleic acid probe.

[0048] A solution of 5×SSC or 3 M tetramethylammonium chloride is added onto the substrate and heated (usually 37-50° C.) to remove oligonucleotides that form a nonspecific hybrid or do not form specific hybrid from the substrate so that only specific hybrids should be selectively left on the substrate.

[0049] The hybrids are detected by using the fluorescence substance or hapten introduced into the nucleic acid probe. When a hapten is used, a solution containing a conjugate of a protein that recognizes the hapten or protein that bonds to the hapten and alkaline phosphatase, horseradish peroxidase or the like (enzyme conjugate) is added onto the substrate and allowed to react at room temperature for several dozens of minutes. A nonspecific adsorption reaction of the enzyme conjugate and the substrate can be prevented by completely coating regions on the substrate with a protein such as BSA except for the regions in which the oligonucleotides are immobilized before a bonding reaction of the hapten and the enzyme conjugate is performed. This treatment can be performed by, after the oligonucleotides are immobilized, adding a solution of a protein such as BSA onto the substrate and leaving it at room temperature for several dozens of minutes. After the bonding reaction of the enzyme conjugate and the hapten of the nucleic acid probe is completed, only enzyme conjugates that bond to the hapten in the nucleic acid probe are left on the substrate by washing the substrate with an appropriate buffer containing a surfactant to remove enzyme conjugates that did not bond to the hapten.

[0050] In order to visualize the hybrids, a compound that becomes insoluble only when only a bonding product of the hapten and the enzyme conjugate exists is added. The production of the insoluble compound is amplified by the enzymatic reaction, and thus the hybrids are visualized. As the compound used for this purpose, nitroblue tetrazolium chloride (NBT) and 5-bromo-4-chloro-3-indolyl phosphate, p-toluidine salt (BCIP) are used when the enzyme in the enzyme conjugate is alkaline phosphatase. When the enzyme is horseradish peroxidase, 3,3′,5,5′-tetramethylbenzidine (TMB) or the like can be used.

[0051] Quinolon resistance of tubercle bacillius is determined based on the obtained results of the hybridization by examining pigmentation or fluorescent color development at positions at which the capture oligos are immobilized.

[0052] The kit of the present invention is a kit for determining quinolon resistance of a tubercle bacillus strain by detecting a mutation in the gyrA gene of the bacterial strain, which includes an oligonucleotide for detecting a substitution of another amino acid residue for an amino acid residue corresponding to the 89th aspartic acid residue in the amino acid sequence encoded by the gyrase A gene. As the oligonucleotide, a capture oligo or a substrate on which the capture oligo is immobilized can be mentioned. Further, the kit of the present invention may include primers for preparing a nucleic acid probe, labeled nucleic acid probe, buffer, reagents for hybridization such as enzyme conjugate that recognizes hapten and so forth.

[0053] As quinolon to which the present invention can be applied, there can be mentioned levofloxacin, ciprofloxacin, ofloxacin, gatifloxacin and so forth.

EXAMPLES

[0054] Hereafter, the present invention will be explained more specifically with reference to the following example.

[0055] <1> Isolation of Quinolon-resistant Strain of Mycobacterium tuberculosis

[0056] Sputum of a tuberculosis patient was applied on Ogawa medium and cultured in an incubator at 37° C. for 4 weeks. Appeared colonies were inoculated again on Ogawa medium containing 2.5 μg/mL of levofloxacin and cultured in an incubator at 37° C. for 4 weeks. The strains that formed colonies were isolated as quinolon-resistant strains.

[0057] <2>Determination of Nucleotide Sequence of gyrA Gene of Quinolon-resistant Strain

[0058] Genomic DNA was prepared from each of the quinolon-resistant strains isolated as described above by the method of Kent et al. (Kent, P. T., et al., Mycobacteriology, A Guide for the Level III Laboratory, p.31, U.S. Department of Health and Human Service, Public Health Service, Center for Disease Control, 1985). PCR was performed for the obtained genome by using primers having the nucleotide sequences shown as SEQ ID NOS: 5 and 6.

[0059] rTaq (Takara Shuzo) was used for PCR. PCR was performed by a reaction at 98° C. for 1 minute, 35 cycles of reactions at 98° C. for 5 seconds, at 55° C. for 10 seconds and at 72° C. for 20 seconds, and a reaction at 72° C. for 1 minute. The amplification product was separated by 1% agarose gel electrophoresis, and a gel containing a 0.4 kbp band was excised. This gel piece was placed into a 1.5-mL micro tube and frozen at −135° C. for 15 minutes. Then, the gel was centrifuged at 15000 rpm for 10 minutes to obtain a supernatant. Resulting DNA solution was used as a template together with a primer shown as SEQ ID NO: 5 and Big Dye Terminator kit manufactured by ABI to perform a sequencing reaction. After completion of the reaction, the sequence was analyzed by using a genetic analyzer manufactured by ABI.

[0060]FIG. 1 shows alignment of the obtained sequences. In FIG. 1, the number shown at the right end of each sequence represents the number of sequences that had the same mutation among the determined sequences. Among these mutations, substitution of A for G at the 530th position in the nucleotide sequence shown as SEQ ID NO: 3 is a novel mutation. Further, substitution of A for G at the 530th position and substitution of A for G at the 545th position constitute a novel combination of mutations. Other mutations were the same as the mutations already reported (Antimicrob. Agents Chemother., 1996, 40 (8), 1768-1774; J. Infect. Dis., 1996, 174, 1127-1130; Eur. J. Clin. Microbiol. Infect. Dis., 1997, 16, 395-398; J. Infect. Dis., 2000, 182, 517-525).

1 6 1 50 DNA Mycobacterium tuberculosis CDS (2)..(49) 1 c aac tac cac ccg cac ggc gac gcg tcg atc tac gac agc ctg gtg cgc 49 Asn Tyr His Pro His Gly Asp Ala Ser Ile Tyr Asp Ser Leu Val Arg 1 5 10 15 a 50 2 16 PRT Mycobacterium tuberculosis 2 Asn Tyr His Pro His Gly Asp Ala Ser Ile Tyr Asp Ser Leu Val Arg 1 5 10 15 3 2884 DNA Mycobacterium tuberculosis CDS (266)..(2782) 3 aagatcaaca aggaagacgg cattcagcgg tacaagggtc taggtgaaat ggacgctaag 60 gagttgtggg agaccaccat ggatccctcg gttcgtgtgt tgcgtcaagt gacgctggac 120 gacgccgccg ccgccgacga gttgttctcc atcctgatgg gcgaggacgt cgacgcgcgg 180 cgcagcttta tcacccgcaa cgccaaggat gttcggttcc tggatgtcta acgcaaccct 240 gcgttcgatt gcaaacgagg aatag atg aca gac acg acg ttg ccg cct gac 292 Met Thr Asp Thr Thr Leu Pro Pro Asp 1 5 gac tcg ctc gac cgg atc gaa ccg gtt gac atc gag cag gag atg cag 340 Asp Ser Leu Asp Arg Ile Glu Pro Val Asp Ile Glu Gln Glu Met Gln 10 15 20 25 cgc agc tac atc gac tat gcg atg agc gtg atc gtc ggc cgc gcg ctg 388 Arg Ser Tyr Ile Asp Tyr Ala Met Ser Val Ile Val Gly Arg Ala Leu 30 35 40 ccg gag gtg cgc gac ggg ctc aag ccc gtg cat cgc cgg gtg ctc tat 436 Pro Glu Val Arg Asp Gly Leu Lys Pro Val His Arg Arg Val Leu Tyr 45 50 55 gca atg ttc gat tcc ggc ttc cgc ccg gac cgc agc cac gcc aag tcg 484 Ala Met Phe Asp Ser Gly Phe Arg Pro Asp Arg Ser His Ala Lys Ser 60 65 70 gcc cgg tcg gtt gcc gag acc atg ggc aac tac cac ccg cac ggc gac 532 Ala Arg Ser Val Ala Glu Thr Met Gly Asn Tyr His Pro His Gly Asp 75 80 85 gcg tcg atc tac gac agc ctg gtg cgc atg gcc cag ccc tgg tcg ctg 580 Ala Ser Ile Tyr Asp Ser Leu Val Arg Met Ala Gln Pro Trp Ser Leu 90 95 100 105 cgc tac ccg ctg gtg gac ggc cag ggc aac ttc ggc tcg cca ggc aat 628 Arg Tyr Pro Leu Val Asp Gly Gln Gly Asn Phe Gly Ser Pro Gly Asn 110 115 120 gac cca ccg gcg gcg atg agg tac acc gaa gcc cgg ctg acc ccg ttg 676 Asp Pro Pro Ala Ala Met Arg Tyr Thr Glu Ala Arg Leu Thr Pro Leu 125 130 135 gcg atg gag atg ctg agg gaa atc gac gag gag aca gtc gat ttc atc 724 Ala Met Glu Met Leu Arg Glu Ile Asp Glu Glu Thr Val Asp Phe Ile 140 145 150 cct aac tac gac ggc cgg gtg caa gag ccg acg gtg cta ccc agc cgg 772 Pro Asn Tyr Asp Gly Arg Val Gln Glu Pro Thr Val Leu Pro Ser Arg 155 160 165 ttc ccc aac ctg ctg gcc aac ggg tca ggc ggc atc gcg gtc ggc atg 820 Phe Pro Asn Leu Leu Ala Asn Gly Ser Gly Gly Ile Ala Val Gly Met 170 175 180 185 gca acc aat atc ccg ccg cac aac ctg cgt gag ctg gcc gac gcg gtg 868 Ala Thr Asn Ile Pro Pro His Asn Leu Arg Glu Leu Ala Asp Ala Val 190 195 200 ttc tgg gcg ctg gag aat cac gac gcc gac gaa gag gag acc ctg gcc 916 Phe Trp Ala Leu Glu Asn His Asp Ala Asp Glu Glu Glu Thr Leu Ala 205 210 215 gcg gtc atg ggg cgg gtt aaa ggc ccg gac ttc ccg acc gcc gga ctg 964 Ala Val Met Gly Arg Val Lys Gly Pro Asp Phe Pro Thr Ala Gly Leu 220 225 230 atc gtc gga tcc cag ggc acc gct gat gcc tac aaa act ggc cgc ggc 1012 Ile Val Gly Ser Gln Gly Thr Ala Asp Ala Tyr Lys Thr Gly Arg Gly 235 240 245 tcc att cga atg cgc gga gtt gtt gag gta gaa gag gat tcc cgc ggt 1060 Ser Ile Arg Met Arg Gly Val Val Glu Val Glu Glu Asp Ser Arg Gly 250 255 260 265 cgt acc tcg ctg gtg atc acc gag ttg ccg tat cag gtc aac cac gac 1108 Arg Thr Ser Leu Val Ile Thr Glu Leu Pro Tyr Gln Val Asn His Asp 270 275 280 aac ttc atc act tcg atc gcc gaa cag gtc cga gac ggc aag ctg gcc 1156 Asn Phe Ile Thr Ser Ile Ala Glu Gln Val Arg Asp Gly Lys Leu Ala 285 290 295 ggc att tcc aac att gag gac cag tct agc gat cgg gtc ggt tta cgc 1204 Gly Ile Ser Asn Ile Glu Asp Gln Ser Ser Asp Arg Val Gly Leu Arg 300 305 310 atc gtc atc gag atc aag cgc gat gcg gtg gcc aag gtg gtg atc aat 1252 Ile Val Ile Glu Ile Lys Arg Asp Ala Val Ala Lys Val Val Ile Asn 315 320 325 aac ctt tac aag cac acc cag ctg cag acc agc ttt ggc gcc aac atg 1300 Asn Leu Tyr Lys His Thr Gln Leu Gln Thr Ser Phe Gly Ala Asn Met 330 335 340 345 cta gcg atc gtc gac ggg gtg ccg cgc acg ctg cga ctg gac cag ctg 1348 Leu Ala Ile Val Asp Gly Val Pro Arg Thr Leu Arg Leu Asp Gln Leu 350 355 360 atc cgc tat tac gtt gac cac caa ctc gac gtc att gtg cgg cgc acc 1396 Ile Arg Tyr Tyr Val Asp His Gln Leu Asp Val Ile Val Arg Arg Thr 365 370 375 acc tac cgg ctg cgc aag gca aac gag cga gcc cac att ctg cgc ggc 1444 Thr Tyr Arg Leu Arg Lys Ala Asn Glu Arg Ala His Ile Leu Arg Gly 380 385 390 ctg gtt aaa gcg ctc gac gcg ctg gac gag gtc att gca ctg atc cgg 1492 Leu Val Lys Ala Leu Asp Ala Leu Asp Glu Val Ile Ala Leu Ile Arg 395 400 405 gcg tcg gag acc gtc gat atc gcc cgg gcc gga ctg atc gag ctg ctc 1540 Ala Ser Glu Thr Val Asp Ile Ala Arg Ala Gly Leu Ile Glu Leu Leu 410 415 420 425 gac atc gac gag atc cag gcc cag gca atc ctg gac atg cag ttg cgg 1588 Asp Ile Asp Glu Ile Gln Ala Gln Ala Ile Leu Asp Met Gln Leu Arg 430 435 440 cgc ctg gcc gca ctg gaa cgc cag cgc atc atc gac gac ctg gcc aaa 1636 Arg Leu Ala Ala Leu Glu Arg Gln Arg Ile Ile Asp Asp Leu Ala Lys 445 450 455 atc gag gcc gag atc gcc gat ctg gaa gac atc ctg gca aaa ccc gag 1684 Ile Glu Ala Glu Ile Ala Asp Leu Glu Asp Ile Leu Ala Lys Pro Glu 460 465 470 cgg cag cgt ggg atc gtg cgc gac gaa ctc gcc gaa atc gtg gac agg 1732 Arg Gln Arg Gly Ile Val Arg Asp Glu Leu Ala Glu Ile Val Asp Arg 475 480 485 cac ggc gac gac cgg cgt acc cgg atc atc gcg gcc gac gga gac gtc 1780 His Gly Asp Asp Arg Arg Thr Arg Ile Ile Ala Ala Asp Gly Asp Val 490 495 500 505 agc gac gag gat ttg atc gcc cgc gag gac gtc gtt gtc act atc acc 1828 Ser Asp Glu Asp Leu Ile Ala Arg Glu Asp Val Val Val Thr Ile Thr 510 515 520 gaa acg gga tac gcc aag cgc acc aag acc gat ctg tat cgc agc cag 1876 Glu Thr Gly Tyr Ala Lys Arg Thr Lys Thr Asp Leu Tyr Arg Ser Gln 525 530 535 aaa cgc ggc ggc aag ggc gtg cag ggt gcg ggg ttg aag cag gac gac 1924 Lys Arg Gly Gly Lys Gly Val Gln Gly Ala Gly Leu Lys Gln Asp Asp 540 545 550 atc gtc gcg cac ttc ttc gtg tgc tcc acc cac gat ttg atc ctg ttc 1972 Ile Val Ala His Phe Phe Val Cys Ser Thr His Asp Leu Ile Leu Phe 555 560 565 ttc acc acc cag gga cgg gtt tat cgg gcc aag gcc tac gac ttg ccc 2020 Phe Thr Thr Gln Gly Arg Val Tyr Arg Ala Lys Ala Tyr Asp Leu Pro 570 575 580 585 gag gcc tcc cgg acg gcg cgc ggg cag cac gtg gcc aac ctg tta gcc 2068 Glu Ala Ser Arg Thr Ala Arg Gly Gln His Val Ala Asn Leu Leu Ala 590 595 600 ttc cag ccc gag gaa cgc atc gcc cag gtc atc cag att cgc ggc tac 2116 Phe Gln Pro Glu Glu Arg Ile Ala Gln Val Ile Gln Ile Arg Gly Tyr 605 610 615 acc gac gcc ccg tac ctg gtg ctg gcc act cgc aac ggg ctg gtg aaa 2164 Thr Asp Ala Pro Tyr Leu Val Leu Ala Thr Arg Asn Gly Leu Val Lys 620 625 630 aag tcc aag ctg acc gac ttc gac tcc aat cgc tcg ggc gga atc gtg 2212 Lys Ser Lys Leu Thr Asp Phe Asp Ser Asn Arg Ser Gly Gly Ile Val 635 640 645 gcg gtc aac ctg cgc gac aac gac gag ctg gtc ggt gcg gtg ctg tgt 2260 Ala Val Asn Leu Arg Asp Asn Asp Glu Leu Val Gly Ala Val Leu Cys 650 655 660 665 tcg gcc ggc gac gac ctg ctg ctg gtc tcg gcc aac ggg cag tcc atc 2308 Ser Ala Gly Asp Asp Leu Leu Leu Val Ser Ala Asn Gly Gln Ser Ile 670 675 680 agg ttc tcg gcg acc gac gag gcg ctg cgg cca atg ggt cgt gcc acc 2356 Arg Phe Ser Ala Thr Asp Glu Ala Leu Arg Pro Met Gly Arg Ala Thr 685 690 695 tcg ggt gtg cag ggc atg cgg ttc aat atc gac gac cgg ctc gtg tcg 2404 Ser Gly Val Gln Gly Met Arg Phe Asn Ile Asp Asp Arg Leu Val Ser 700 705 710 ctg aac gtc gtg cgt gaa ggc acc tat ctg ctg gtg gcg acg tca ggg 2452 Leu Asn Val Val Arg Glu Gly Thr Tyr Leu Leu Val Ala Thr Ser Gly 715 720 725 ggc tat gcg aaa cgt acc gcg atc gag gaa tac ccg gta cag ggc cgc 2500 Gly Tyr Ala Lys Arg Thr Ala Ile Glu Glu Tyr Pro Val Gln Gly Arg 730 735 740 745 ggc ggt aaa ggt gtg ctg acg gtc atg tac gac cgc cgg cgc ggc agg 2548 Gly Gly Lys Gly Val Leu Thr Val Met Tyr Asp Arg Arg Arg Gly Arg 750 755 760 ttg gtt ggg gcg ttg att gtc gac gac gac agc gag ctg tat gcc gtc 2596 Leu Val Gly Ala Leu Ile Val Asp Asp Asp Ser Glu Leu Tyr Ala Val 765 770 775 act tcc ggc ggt ggc gtg atc cgc acc gcg gca cgc cag gtt cgc aag 2644 Thr Ser Gly Gly Gly Val Ile Arg Thr Ala Ala Arg Gln Val Arg Lys 780 785 790 gcg gga cgg cag acc aag ggt gtt cgg ttg atg aat ctg ggc gag ggc 2692 Ala Gly Arg Gln Thr Lys Gly Val Arg Leu Met Asn Leu Gly Glu Gly 795 800 805 gac aca ctg ttg gcc atc gcg cgc aac gcc gaa gaa agt ggc gac gat 2740 Asp Thr Leu Leu Ala Ile Ala Arg Asn Ala Glu Glu Ser Gly Asp Asp 810 815 820 825 aat gcc gtg gac gcc aac ggc gca gac cag acg ggc aat taa 2782 Asn Ala Val Asp Ala Asn Gly Ala Asp Gln Thr Gly Asn 830 835 tcaggctcgc ccgacgacga tgcggatcgc gtagcgatct gaggaggaat cgggcagcta 2842 ggctcggcag ccgggtacga gtgttaggag tcggggtgac tg 2884 4 838 PRT Mycobacterium tuberculosis 4 Met Thr Asp Thr Thr Leu Pro Pro Asp Asp Ser Leu Asp Arg Ile Glu 1 5 10 15 Pro Val Asp Ile Glu Gln Glu Met Gln Arg Ser Tyr Ile Asp Tyr Ala 20 25 30 Met Ser Val Ile Val Gly Arg Ala Leu Pro Glu Val Arg Asp Gly Leu 35 40 45 Lys Pro Val His Arg Arg Val Leu Tyr Ala Met Phe Asp Ser Gly Phe 50 55 60 Arg Pro Asp Arg Ser His Ala Lys Ser Ala Arg Ser Val Ala Glu Thr 65 70 75 80 Met Gly Asn Tyr His Pro His Gly Asp Ala Ser Ile Tyr Asp Ser Leu 85 90 95 Val Arg Met Ala Gln Pro Trp Ser Leu Arg Tyr Pro Leu Val Asp Gly 100 105 110 Gln Gly Asn Phe Gly Ser Pro Gly Asn Asp Pro Pro Ala Ala Met Arg 115 120 125 Tyr Thr Glu Ala Arg Leu Thr Pro Leu Ala Met Glu Met Leu Arg Glu 130 135 140 Ile Asp Glu Glu Thr Val Asp Phe Ile Pro Asn Tyr Asp Gly Arg Val 145 150 155 160 Gln Glu Pro Thr Val Leu Pro Ser Arg Phe Pro Asn Leu Leu Ala Asn 165 170 175 Gly Ser Gly Gly Ile Ala Val Gly Met Ala Thr Asn Ile Pro Pro His 180 185 190 Asn Leu Arg Glu Leu Ala Asp Ala Val Phe Trp Ala Leu Glu Asn His 195 200 205 Asp Ala Asp Glu Glu Glu Thr Leu Ala Ala Val Met Gly Arg Val Lys 210 215 220 Gly Pro Asp Phe Pro Thr Ala Gly Leu Ile Val Gly Ser Gln Gly Thr 225 230 235 240 Ala Asp Ala Tyr Lys Thr Gly Arg Gly Ser Ile Arg Met Arg Gly Val 245 250 255 Val Glu Val Glu Glu Asp Ser Arg Gly Arg Thr Ser Leu Val Ile Thr 260 265 270 Glu Leu Pro Tyr Gln Val Asn His Asp Asn Phe Ile Thr Ser Ile Ala 275 280 285 Glu Gln Val Arg Asp Gly Lys Leu Ala Gly Ile Ser Asn Ile Glu Asp 290 295 300 Gln Ser Ser Asp Arg Val Gly Leu Arg Ile Val Ile Glu Ile Lys Arg 305 310 315 320 Asp Ala Val Ala Lys Val Val Ile Asn Asn Leu Tyr Lys His Thr Gln 325 330 335 Leu Gln Thr Ser Phe Gly Ala Asn Met Leu Ala Ile Val Asp Gly Val 340 345 350 Pro Arg Thr Leu Arg Leu Asp Gln Leu Ile Arg Tyr Tyr Val Asp His 355 360 365 Gln Leu Asp Val Ile Val Arg Arg Thr Thr Tyr Arg Leu Arg Lys Ala 370 375 380 Asn Glu Arg Ala His Ile Leu Arg Gly Leu Val Lys Ala Leu Asp Ala 385 390 395 400 Leu Asp Glu Val Ile Ala Leu Ile Arg Ala Ser Glu Thr Val Asp Ile 405 410 415 Ala Arg Ala Gly Leu Ile Glu Leu Leu Asp Ile Asp Glu Ile Gln Ala 420 425 430 Gln Ala Ile Leu Asp Met Gln Leu Arg Arg Leu Ala Ala Leu Glu Arg 435 440 445 Gln Arg Ile Ile Asp Asp Leu Ala Lys Ile Glu Ala Glu Ile Ala Asp 450 455 460 Leu Glu Asp Ile Leu Ala Lys Pro Glu Arg Gln Arg Gly Ile Val Arg 465 470 475 480 Asp Glu Leu Ala Glu Ile Val Asp Arg His Gly Asp Asp Arg Arg Thr 485 490 495 Arg Ile Ile Ala Ala Asp Gly Asp Val Ser Asp Glu Asp Leu Ile Ala 500 505 510 Arg Glu Asp Val Val Val Thr Ile Thr Glu Thr Gly Tyr Ala Lys Arg 515 520 525 Thr Lys Thr Asp Leu Tyr Arg Ser Gln Lys Arg Gly Gly Lys Gly Val 530 535 540 Gln Gly Ala Gly Leu Lys Gln Asp Asp Ile Val Ala His Phe Phe Val 545 550 555 560 Cys Ser Thr His Asp Leu Ile Leu Phe Phe Thr Thr Gln Gly Arg Val 565 570 575 Tyr Arg Ala Lys Ala Tyr Asp Leu Pro Glu Ala Ser Arg Thr Ala Arg 580 585 590 Gly Gln His Val Ala Asn Leu Leu Ala Phe Gln Pro Glu Glu Arg Ile 595 600 605 Ala Gln Val Ile Gln Ile Arg Gly Tyr Thr Asp Ala Pro Tyr Leu Val 610 615 620 Leu Ala Thr Arg Asn Gly Leu Val Lys Lys Ser Lys Leu Thr Asp Phe 625 630 635 640 Asp Ser Asn Arg Ser Gly Gly Ile Val Ala Val Asn Leu Arg Asp Asn 645 650 655 Asp Glu Leu Val Gly Ala Val Leu Cys Ser Ala Gly Asp Asp Leu Leu 660 665 670 Leu Val Ser Ala Asn Gly Gln Ser Ile Arg Phe Ser Ala Thr Asp Glu 675 680 685 Ala Leu Arg Pro Met Gly Arg Ala Thr Ser Gly Val Gln Gly Met Arg 690 695 700 Phe Asn Ile Asp Asp Arg Leu Val Ser Leu Asn Val Val Arg Glu Gly 705 710 715 720 Thr Tyr Leu Leu Val Ala Thr Ser Gly Gly Tyr Ala Lys Arg Thr Ala 725 730 735 Ile Glu Glu Tyr Pro Val Gln Gly Arg Gly Gly Lys Gly Val Leu Thr 740 745 750 Val Met Tyr Asp Arg Arg Arg Gly Arg Leu Val Gly Ala Leu Ile Val 755 760 765 Asp Asp Asp Ser Glu Leu Tyr Ala Val Thr Ser Gly Gly Gly Val Ile 770 775 780 Arg Thr Ala Ala Arg Gln Val Arg Lys Ala Gly Arg Gln Thr Lys Gly 785 790 795 800 Val Arg Leu Met Asn Leu Gly Glu Gly Asp Thr Leu Leu Ala Ile Ala 805 810 815 Arg Asn Ala Glu Glu Ser Gly Asp Asp Asn Ala Val Asp Ala Asn Gly 820 825 830 Ala Asp Gln Thr Gly Asn 835 5 23 DNA Mycobacterium tuberculosis CDS (2)..(49) 5 agcgcagcta catcgactat gcg 23 6 23 DNA Mycobacterium tuberculosis CDS (2)..(49) 6 cttcggtgta cctcatcgcc gcc 23 

What is claimed is:
 1. A method for determining quinolon resistance of a Mycobacterium tuberculosis strain comprising detecting a mutation in a gyrase A gene of the bacterial strain, wherein the mutation is substitution of another amino acid residue for an amino acid residue corresponding to the 89th aspartic acid residue in the amino acid sequence encoded by the gyrase A gene.
 2. The method according to claim 1, wherein the other amino acid residue is an asparagine residue.
 3. The method according to claim 1 or 2, wherein the amino acid sequence encoded by the gyrase A gene is the amino acid sequence of SEQ ID NO: 4 or an amino acid sequence of SEQ ID NO: 4 including substitution, deletion or insertion of one or several amino acid residues.
 4. The method according to any one of claims 1 to 3, wherein the mutation is substitution of T for G that is the first nucleotide of a codon coding for an aspartic acid residue.
 5. The method according to claim 4, wherein the mutation occurs at a position corresponding to the 530th nucleotide in the nucleotide sequence of SEQ ID NO:
 3. 6. The method according to any one of claims 1 to 5, further comprising detecting a substitution of A for a base corresponding to G at the 545th position in the nucleotide sequence of SEQ ID NO:
 3. 7. A kit for determining quinolon resistance of a Mycobacterium tuberculosis strain by detecting a mutation in a gyrase A gene of the bacterial strain, comprising an oligonucleotide for detecting a substitution of another amino acid residue for an amino acid residue corresponding to the 89th aspartic acid residue in an amino acid sequence encoded by the gyrase A gene. 